Hydrogen-bonded Configurations Research Articles

Influence of hydrogen-bonding configurations on the physical properties of hydrogenated amorphous silicon.

We analyzed the physical properties of hydrogenated amorphous silicon (a-Si:H) samples grown by plasma-enhanced chemical vapor deposition, by means of infrared spectroscopy, mass-density, and optical measurements. We applied the usual infrared spectroscopic techniques to evaluate the amount of incorporated hydrogen and to investigate the influence of the Si-H bonding configurations on the optical and electronic properties of a-Si:H obtained by this widely used deposition process, and with parameters so chosen as to obtain films having state of the art characteristics. We carried out an exhaustive study of the different infrared absorption peaks, generally ascribed to different bonding configurations of H in Si, with a view to distinguishing the different contributions of SiH, ${\mathrm{SiH}}_{2}$ (${\mathrm{SiH}}_{2}$${)}_{\mathit{n}}$ to the spectral response of the material and to relating them to deposition temperature. The correlation of this infrared spectral analysis with mass-density measurements has evidenced that, for hydrogen content below 10 at. %, isolated SiH and ${\mathrm{SiH}}_{2}$ bonds occur, whereas, with higher hydrogen concentrations, the formation of (${\mathrm{SiH}}_{2}$${)}_{\mathit{n}}$ chains gives rise to empty cavities where hydrogen is preferentially incorporated. In addition, optical measurements show that samples deposited at temperatures below 170 \ifmmode^\circ\else\textdegree\fi{}C exhibit energy gaps and defect densities, which are quite different to those expected if only the effects of SiH groups are considered.

Correlation between short-range order and hydrogen bonding in hydrogenated amorphous silicon obtained by homogeneous chemical vapour deposition

Abstract In the present work the hydrogen-bonding configuration of hydrogenated amorphous silicon obtained by homogeneous chemical vapour deposition is studied as a function of the substrate temperature. The hydrogen concentration and its bonding configuration have been established using infrared spectroscopy measurements. A decrease in the hydrogen concentration with increasing substrate temperature is observed, and this change is due to a decrease in the amount of hydrogen in the dihydride and polyhydride bonding configurations. The film structure has been examined by Raman spectroscopy and the position and the line width of the transverse-optical like phonon band have been used as characteristic parameters for network perfection. A correlation between network perfection and hydrogen-bonding configuration is observed. The most favourable substrate temperature with regard to the film perfection is estimated to be about 300°C.

Linus Pauling 1901–1994

Linus Pauling 1901–1994

Low temperature crystal structure and molecular conformation of l-(+)-lactic acid

Abstract l -(+)-Lactic acid, C3H6O3, M = 90.08, orthorhombic, P212121, a = 5.4896(3), b = 8.4221(3), c = 9.3453(5)A, V = 432.07(4)A3, Z = 4, Dx = 1.385 g cm−1, λ(MoKα) = 0.71073 A, μ = 1.2cm−1, F(000) = 192. Diffraction data have been collected at 100 K and the structure has been solved by direct methods to R = 0.030 for 976 unique observed data. The hydroxyacetic acid moiety of the molecule is almost planar with the aliphatic hydroxy-group oxygen atom at the side of the carbonyl oxygen atom of the carboxy group. The two hydroxy groups are involved in intermolecular hydrogen bonding. The aliphatic hydroxy group forms a bifurcate planar hydrogen-bond configuration in which the aliphatic hydroxy and acid carbonyl oxygen atoms of a symmetry-related molecule participate as acceptors. The acidic hydroxy group donates an intermolecular hydrogen bond to the aliphatic hydroxy-group oxygen atom.

Stability of a model beta-sheet in water.

We have used molecular dynamics simulations to determine the stability in water of a model beta-sheet formed by two alanine dipeptide molecules with two intermolecular hydrogen bonds in the closely spaced antiparallel arrangement. In this paper we describe our computations of the binding free energy of the model sheet and a portion of the free energy surface as a function of a reaction co-ordinate for sheet formation. We used the free energy surface to identify stable conformations along the reaction co-ordinate. To determine whether or not the model sheet with two hydrogen bonds is more stable than a single amide hydrogen bond in water, we compared the results of the present calculations to results from our earlier study of linear hydrogen bond formation between two formamide molecules (the formamide "dimer"). The free energy surfaces for the sheet and formamide dimer each have two minima corresponding to locally stable hydrogen-bonded and solvent-separated configurations. The binding free energies of the model sheet and the formamide dimer are -5.5 and -0.34 kcal/mol, respectively. Thus, the model sheet with two hydrogen bonds is quite stable while the simple amide hydrogen bond is only marginally stable. To understand the relative stabilities of the model sheet and formamide dimer in terms of solute-solute and solute-water interactions, we decomposed the free energy differences between hydrogen-bonded and solvent-separated conformations into energetic and entropic contributions. The changes in the peptide-peptide energy and the entropy are roughly twice as large for the sheet as they are for the formamide dimer. The magnitude of the peptide-water energy difference for the sheet is less than twice (by about 3.5 kcal/mol) that for the formamide dimer, and this accounts for the stability of the sheet. The presence of the side-chains and/or blocking groups apparently prevents the amide groups in the sheet from being solvated as favorably in the separated arrangement as in the formamide dimer, where the amide groups are completely exposed to the solvent.

Towards an understanding of the arginine-aspartate interaction

We have made a comparison of the geometries of intra- and intermolecular arginine-aspartate interactions by extracting orientation information from protein co-ordinate data. The results show a pronounced difference, with both types of interaction preferring to form twin NH … OC hydrogen bonds, but involving different nitrogen atoms. In intramolecular interactions, the aspartate favours a “side on” geometry, forming hydrogen bonds with N ε and N η2; in the intermolecular case, however, “end on” contacts involving N η1 and N η2 of the arginine are preferred. We have used Distributed Multipole Analysis of the methylguanidinium-acetate system to model the electrostatic component of the arginine-aspartate ion pair interaction in vacuo. We find, in agreement with the experimental arginine-aspartate distribution, that side on and end on doubly NH … OC hydrogen-bonded configurations are clearly the most favourable, with the side on being marginally lower in energy. Thus, despite the many competing side-chain interactions in proteins, many arginine-aspartate pairs adopt one of the minimum electrostatic energy conformations, or one close to a minimum. Within each of the two regions (side on and end on) we find only a small energy gap between the “symmetric” doubly hydrogen-bonded and slightly displaced “staggered” structures, again in agreement with the crystal structure data. Further calculations of the total ab initio interaction energy show that this follows the electrostatic term in its orientational variation, this phenomenon of “electrostatic domination” being well known in hydrogen-bonded systems. The end on arginine nitrogen atoms are observed to be more surface-exposed than N ε, as demonstrated by their greater accessibilities over a large sample of proteins. This helps explain the side on and end on preferences of intra- and intermolecular interactions, respectively. We also note the effect of short sequence intervals, particularly i 3 i + 2 relationships, in forcing many intramolecular contacts to be side on.

Spectroscopic and crystallographic study of 27,28-diethoxy- p-tert-butylcalix[4]arenes

C 48H 64O 4, M r = 705.04, monoclinic, P2 1/ n, a= 14.509(2) Å, b = 17.913(4) Å, c = 16.899(1) Å, β = 107.343(9)°, V = 4192.4(11) Å 3, Z = 4, D x = 1.117 g cm −3, λ(Mo Kα) = 0.71073 Å, μ = 0.74 cm −1, F(000) = 1536, T = 100 K, R = 0.059 for 5505 observed reflections with I& >; 2.5σ( I). The molecular conformation of the anti form of the title compound, i.e. with the two neighbouring phenylethylether fragments in anti positions, is a partial cone. The conformation is stabilized by two intramolecular hydrogen bonds. These bonds involve both the phenolic OH groups as donors and a hydroxyl group and an ethoxygroup as acceptors. FT-IR solid state spectra reveal two OH bands at 3388 and 3175 cm −1 which is in accordance with the observed hydrogen-bond configuration. In CCl 4 solution the partial cone is preserved for the anti form (3378 and 3187 cm −1) while the corresponding syn form mainly adopts a cone conformation characterized by OH stretching vibrations at 3360 and 3168 cm −1.

Multiphoton ionization studies of clusters of immiscible liquids. II. C6H6–(H2O)n, n=3–8 and (C6H6)2–(H2O)1,2

Resonant two-photon ionization (R2PI) time-of-flight mass spectroscopy is used to record S0–S1 spectra of the neutral complexes C6H6–(H2O)n with n=3–8 and (C6H6)2–(H2O)1,2. Due to limitations imposed by the size of these clusters, a number of vibronic level arguments are used to constrain the gross features of the geometries of these clusters. Among the spectral clues provided by the data are the frequency shifts of the transitions, their van der Waals structure, the fragmentation of the photoionized clusters, and the complexation-induced origin intensity and 610 splitting. In the 1:3 cluster, simple arguments are made based on the known structures of the 1:1 and 1:2 clusters which lead to the conclusion that all three water molecules reside on the same side of the benzene ring. Three structures for the 1:3 cluster are proposed which are consistent with the available data. Of these, only one is also consistent with the remarkable similarity of the 1:4 and 1:5 spectra to those of the 1:3 cluster. This structure involves a cyclic water trimer in which one of the water molecules is near the sixfold axis in a π hydrogen-bonded configuration. This structure is then expanded in the 1:4 and 1:5 clusters to incorporate the fourth and fifth water molecules in cyclic structures which place the additional water molecules far from the benzene ring without disturbing the interaction of the other water molecules with the benzene ring. For 1:n clusters with n≥6, subtle and then significant changes are observed in the spectra which indicate changes in the way the water cluster interacts with the benzene ring. This development occurs at precisely the water cluster size which calculations predict that cagelike water cluster structures will begin to compete and eventually be favored over large cyclic structures. Finally, cursory scans of the 2:1 cluster show that this cluster also fragments efficiently upon photoionization by loss of a single water molecule and that it possesses a distinctly asymmetric structure with a sizable 610 splitting. Two potential structures are proposed for the 2:1 cluster which can both reasonably explain the observations—a BBW structure in which the water molecule (W) is π hydrogen bonded to a single benzene molecule (B) and a BWB structure in which the water molecule bridges the two benzenes via π hydrogen bonds to both.

New spectroscopy of water using tunable picosecond pulses in the infrared

Spectral hole burning is observed for the OH stretching mode of HDO dissolved in ${\mathrm{D}}_{2}$O at 298 K after intense infrared excitation. Three spectral components are inferred from the transient band shapes and related to an icelike molecular environment and other hydrogen-bonding configurations. A population lifetime of ${\mathit{T}}_{1}$=8\ifmmode\pm\else\textpm\fi{}2 ps and an anharmonic frequency shift of 270\ifmmode\pm\else\textpm\fi{}20 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ are measured.

Hydrogen-bond networks in supercooled liquid water and amorphous/vitreous ices

The structural characteristics of hydrogen bonding in water and ices can be studied by neutron diffraction. This short review concerns recent work on temperature variation and isotopic substitution measurements for the normal and supercooled liquid phase with additional data for solid phases prepared by vapour-deposition and hyperquenched processes. The combined data suggest that the behaviour of low-temperature water can be understood in terms of a systematic evolution of local hydrogen-bonded configurations towards the continuous random hydrogen-bonded network of the amorphous/vitreous ices.

The stereochemistry of the water molecules in the hydrates of small biological molecules

An examination of the stereochemistry of the water molecules in the hydrates of amino acids and peptides, carbohydrates, purines and pyrimidines, and nucleosides and nucleotides, reveals a variety of hydrogen-bonded configurations within a radius of 3.0 A from the water oxygen atom. Water molecules which accept one hydrogen bond are more common than those that accept two, by a factor of 1.4. There are nine examples where the water is not a hydrogen-bond acceptor, but only one where it does not donate two hydrogen bonds. Of the 621 OWH...A bonds examined, 15% were three centered and 2% were four centered or three-center bifurcated. The amino-acid and peptide hydrates displayed the greatest variety with 15 different hydrogen-bond configurations. The coordination of the donor and acceptor atoms within 3.0 A of the water oxygen atom ranged from two to seven.

Controlling hydrogen contents and bond configurations for high-quality and high-reliability a-Si films

We previously reported that a reduction of SiH 2 bond density in the i-layer effectively prevents light-induced degradation of a-Si solar cells. For further reduction of SiH 2 bond density, we fabricate a-Si films at higher substrate temperature (Ts:250 ∼ 400°C) with a glow discharge method by using super chamber. SiH 2 bond density can be reduced to about 10 20cm −3, and highly photoconductive and stable a-Si films are obtained. As a new attempt to reduce SiH 2 bond density, we have investigated an ion-gun CVD method. Hydrogen bond configurations are found to be strongly affected by the accelerating voltage of ions.

Lifetime distributions and anisotropy decays of indole fluorescence in cyclohexane/ethanol mixtures by frequency-domain fluorometry.

We used frequency-domain fluorometry to measure intensity and anisotropy decay of indole fluorescence in cyclohexane/ethanol mixtures at 20 degrees C. In 100% cyclohexane or 100% ethanol the intensity decay of indole appears to be a single exponential with decay times of 7.66 and 4.10 ns, respectively. In cyclohexane containing a small percentage of ethanol (up to 10%), we observed increased heterogeneity in intensity decay, resulting in a 10-fold increase in chi 2R for the single-exponential fit, as compared with the double-exponential model. We obtained comparable or better fits using unimodal Lorentzian and Gaussian lifetime distributions (two floating parameters) than for the two-exponential model (three floating parameters). We believe that the distribution of decay times reflects a range of indole solvation states in the dominately nonpolar solutions. This result suggests that a variety of hydrogen-bonding configurations could be one origin of the distributions of decay times observed for tryptophan emission from proteins. We also measured rotational diffusion of indole in cyclohexane, ethanol and its mixtures at 20 degrees C. The picosecond correlation times required that the mean decay times be decreased by acrylamide quenching (in ethanol) or energy transfer (in cyclohexane). In ethanol we observed nearly isotropic rotation of indole; in cyclohexane we obtained two correlation times of 17 and 73 ps. The shorter correlation time in cyclohexane appears to be due to the slip boundary condition, which was found to be progressively eliminated by small percentages of ethanol. Hence, hydrogen-bonding interactions appear to have a substantial effect on the rotational dynamics of indole.

Independent control of spin density and hydrogen-bonding configuration in glow-discharge-hydrogenated Si-Ge alloys using a cathode-heating method

The number density of dangling bonds (spin density) and the hydrogen content as well as the hydrogen-bonding configuration were independently controlled in the glow-discharge hydrogenated amorphous Si-Ge alloys using a cathode-heating technique. A tentative mechanism is presented in terms of the top surface process as well as the growth zone.

Optical properties and structure of microcrystalline hydrogenated silicon prepared by radio-frequency magnetron sputtering

We have studied the optical properties of hydrogenated microcrystalline silicon films prepared by rf magnetron sputtering. Spectroscopic ellipsometry (SE) has been used to measure the dielectric spectra in the 1.66–5.6-eV range. Films produced with substrate temperature higher than 200 °C and hydrogen partial pressure ratio equal to 0.5 exhibited a microcrystalline structure. Distinct differences were observed between such films as amorphous and microcrystalline films in their dielectric function spectra and other optical quantities. An energy shift and a broadening of the E1 and E2 transitions for the microcrystalline samples were calculated from the analysis of SE data. It was observed that the rf power and the substrate temperature were the primary factors controlling the microcrystallite formation. A strong density dependence of microcrystallinity was observed, for all the optical parameters investigated. The effect of the hydrogen concentration and the hydrogen-bonding configuration on the optical properties is also discussed.

Conformational differences between α-cyclodextrin in aqueous solution and in crystalline form: A molecular dynamics study

The computer simulation technique of molecular dynamics is a powerful tool to delineate the conformational differences between a molecule in different environments. As an illustration, the difference between an α-cyclodextrin molecule in aqueous solution and in crystalline form is determined. Two molecular dynamics simulations are compared. In one simulation, one α-cyclodextrin form in a “truncated octahedron box” containing 611 water molecules is simulated over 90 picoseconds to mimic the solution structure. In the other simulation, the crystalline form is modelled by a molecular dynamics simulation of four unit cells in space group P2 12 12 1 containing 16 α-cyclodextrin molecules and 96 water molecules over a period of 15 picoseconds. The solution structure of α-cyclodextrin deviates by about 0·1 nm from that in the crystal and shows twice as much mobility of the atoms. The experimentally observed twist of glucose unit 5 out of alignment with the other five glucose units in the α-cyclodextrin torus that is present in the crystal simulation, disappears in the simulation in solution, but the glucosidic torsion angles around the ring remain asymmetric. The hydrogen-bonding patterns in crystal and in solution are rather different. This means that in a crystal structure, the molecule and its (hydration) hydrogen-bonding scheme represent only one static minimum energy picture, whereas the molecular dynamics simulations yield a description of all the many hydrogen-bonding configurations that can occur in solution.

Hydrogen bonding considerations in silica gels

Hydrogen bonding is expected to play an important part in the structural aspects of silica gels. All simple and a number of the more complex hydrogen-bonding configurations involving the proton donors FH and OH interacting with the proton acceptor lone electron pairs on F and O are tabulated. This includes solvent-solvent interactions, solvent molecules hydrogen-bonded to silicon-attached species, and a variety of silicon-silicon bridges involving hydrogen bonds. Ab initio calculations were performed for a number of model structures. Using these as well as literature values in addition to steric considerations, it is possible to assign estimated hydrogen-bonding energy values to various configurations and locate those expected to be dominant. It is found that the presence of fluoride is not expected to change the hydrogen bonding significantly.

Intrinsic stress of phosphorus- and boron-doped amorphous silicon films

Abstract The relationship between the intrinsic stress and hydrogen-bonding configuration for plasma-produced hydrogenated amorphous silicon (a-Si: H) films doped with phosphorus and boron has been studied in the gas-phase doping ratios from 0 to 5 × 10−3 prepared with different substrate temperatures. We found the same strong correlation between the sign and strength of intrinsic stress σi and the infrared stretching-mode absorption ratio I(SiH2)/I(SiH) (= R) as in a previous study on undoped films. The compressive stress rapidly increases as R decreases below 1·2, while the tensile stress increases and finally saturates as R increases above 1·2; consequently, zero stress is reached at R ≊ 1.2. This stress change was found not to be associated with the dopants and the doping levels but with the plasma conditions. The experimental σi-R curve has been interpreted by a phenomenological theory based on a simplified two-phase structural model.

Hydrogen Concentration and Bond Configurations in Silicon Nitride Films Prepared by ECR Plasma CVD Method

The influence of deposition conditions on the hydrogen concentration and bond configurations in silicon nitride (SiN) films prepared by the electron cyclotron resonance plasma CVD(ECR P-CVD) method has been studied in comparison with those prepared by a conventional plasma CVD(P-CVD) method, by means of secondary ion mass spectrometry (SIMS), infrared absorption (IR) spectra and electron spin resonance (ESR). SiN films deposited at low microwave powers and a relatively high SiH4 flow rate had higher H concentrations than those deposited at high microwave powers. The hydrogen concentration was found to be in the range from 1.3×1022-5×1021/cm3 (13.8-4.7%) at microwave powers between 50 and 500 W. The bond configurations in the films are markedly dependent upon the deposition conditions. SiN films with only N-H bonds are thermally stable, even after annealing at 900°C in a dry N2 atmosphere, while almost all the H atoms are lost after annealing for films with both N-N and Si-H bonds. Annealing studies by ESR measurements revealed that the H concentration in the films has little influence on the spin density.

Monte Carlo simulation of an 18.45 mol% aqueous ammonia solution

An intermolecular potential function for ammonia–water has been developed from ab initio molecular-orbital calculations. The analytical potential function consists of Coulomb interaction terms and exponential terms for short-range interactions. A Monte Carlo statistical-mechanics simulation has been carried out for a system containing 48 ammonia molecules and 168 water molecules, corresponding to a 18.45 mol% ammonia solution in water, at 20.0 °C and 1.0 atm. At this concentration the hydrogen-bonded network among water molecules still exists. Analysis of the solvent structure around water molecules suggests that H2O/(H2O)4, (NH3)1 and H2O/(H2O)5, (NH3)1 are the dominant units in the solution, regarding water as the central molecule. The ammonia molecule has 14.6 solvent molecules in the first surrounding shell; the dominant compositions are NH3/(H2O)12, (NH3)2 and NH3/(H2O)13, (NH3)2. NH3/H2O hydrogen-bonded configurations vary considerably in geometry, and H3N⋯H—NH2 bonds are hardly visible.